Journal of Microbiology

Journal Articles

An Optimized Method for Reconstruction of Transcriptional Regulatory Networks in Bacteria Using ChIP-exo and RNA-seq Datasets: Minchang Jang, Joon Young Park, Gayeon Lee, Donghyuk Kim; J. Microbiol. 2024;62(12):1075-1088. Published online November 11, 2024; DOI: https://doi.org/10.1007/s12275-024-00181-6

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Abstract: Transcriptional regulatory networks (TRNs) in bacteria are crucial for elucidating the mechanisms that regulate gene expression and cellular responses to environmental stimuli. These networks delineate the interactions between transcription factors (TFs) and their target genes, thereby uncovering the regulatory processes that modulate gene expression under varying environmental conditions. Analyzing TRNs offers valuable insights into bacterial adaptation, stress responses, and metabolic optimization from an evolutionary standpoint. Additionally, understanding TRNs can drive the development of novel antimicrobial therapies and the engineering of microbial strains for biofuel and bioproduct production. This protocol integrates advanced data analysis pipelines, including ChEAP, DEOCSU, and DESeq2, to analyze omics datasets that encompass genome-wide TF binding sites and transcriptome profiles derived from ChIP-exo and RNA-seq experiments. This approach minimizes both the time required and the risk of bias, making it accessible to non-expert users. Key steps in the protocol include preprocessing and peak calling from ChIP-exo data, differential expression analysis of RNA-seq data, and motif and regulon analysis. This method offers a comprehensive and efficient framework for TRN reconstruction across various bacterial strains, enhancing both the accuracy and reliability of the analysis while providing valuable insights for basic and applied research.

Coumarin-based combined computational study to design novel drugs against Candida albicans: Akhilesh Kumar Maurya , Nidhi Mishra; J. Microbiol. 2022;60(12):1201-1207. Published online November 10, 2022; DOI: https://doi.org/10.1007/s12275-022-2279-5

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Candida species cause the most prevalent fungal illness, candidiasis. Candida albicans is known to cause bloodstream infections. This species is a commensal bacterium, but it can cause hospital–acquired diseases, particularly in COVID-19 patients with impaired immune systems. Candida infections have increased in patients with acute respiratory distress syndrome. Coumarins are both naturally occurring and synthetically produced. In this study, the biological activity of 40 coumarin derivatives was used to create a three-dimensional quantitative structure activity relationship (3D-QSAR) model. The training and test minimum inhibitory concentration values of C. albicans active compounds were split, and a regression model based on statistical data was established. This model served as a foundation for the creation of coumarin derivative QSARs. This is a unique way to create new therapeutic compounds for various ailments. We constructed novel structural coumarin derivatives using the derived QSAR model, and the models were confirmed using molecular docking and molecular dynamics simulation.

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Coumarin derivatives ameliorate the intestinal inflammation and pathogenic gut microbiome changes in the model of infectious colitis through antibacterial activity
Hui-su Jung, Yei Ju Park, Bon-Hee Gu, Goeun Han, Woonhak Ji, Su mi Hwang, Myunghoo Kim
Frontiers in Cellular and Infection Microbiology.2024;[Epub] CrossRef
Therapeutic Effects of Coumarins with Different Substitution Patterns
Virginia Flores-Morales, Ana P. Villasana-Ruíz, Idalia Garza-Veloz, Samantha González-Delgado, Margarita L. Martinez-Fierro
Molecules.2023; 28(5): 2413. CrossRef
Cyclometalated iridium(III) complexes combined with fluconazole: antifungal activity against resistant C. albicans
Jun-Jian Lu, Zhi-Chang Xu, Hou Zhu, Lin-Yuan Zhu, Xiu-Rong Ma, Rui-Rui Wang, Rong-Tao Li, Rui-Rong Ye
Frontiers in Cellular and Infection Microbiology.2023;[Epub] CrossRef

Research Support, Non-U.S. Gov'ts

Role of the extracytoplasmic function sigma factor CarQ in oxidative response of Bradyrhizobium japonicum: Anchana Thaweethawakorn , Dylan Parks , Jae-Seong So , Woo-Suk Chang; J. Microbiol. 2015;53(8):526-534. Published online July 31, 2015; DOI: https://doi.org/10.1007/s12275-015-5308-9

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Abstract

As a nitrogen-fixing bacterium, Bradyrhizobium japonicum can establish a symbiotic relationship with the soybean plant (Glycine max). To be a successful symbiont, B. japonicum must deal with plant defense responses, such as an oxidative burst. Our previous functional genomics study showed that carQ (bll1028) encoding extracytoplasmic function (ECF) sigma factor was highly expressed (107.8-fold induction) under oxidative stress. Little is known about the underlying mechanisms of how CarQ responds to oxidative stress. In this study, a carQ knock-out mutant was constructed using site-specific mutagenesis to identify the role of carQ in the oxidative response of B. japonicum. The carQ mutant showed a longer generation time than the wild type and exhibited significantly decreased survival at 10 mM H2O2 for 10 min of exposure. Surprisingly, there was no significant difference in expression of oxidative stress-responsive genes such as katG and sod between the wild type and carQ mutant. The mutant also showed a significant increase in susceptibility to H2O2 compared to the wild type in the zone inhibition assay. Nodulation phenotypes of the carQ mutant were distinguishable compared to those of the wild type, including lower numbers of nodules, decreased nodule dry weight, decreased plant dry weight, and a lower nitrogen fixation capability. Moreover, desiccation of mutant cells also resulted in significantly lower percent of survival in both early (after 4 h) and late (after 24 h) desiccation periods. Taken together, this information will provide an insight into the role of the ECF sigma factor in B. japonicum to deal with a plant-derived oxidative burst.

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Implication of the σ E Regulon Members OmpO and σ N in the Δ ompA 299–356 -Mediated Decrease of Oxidative Stress Tolerance in St
Ren-Hsuan Ku, Li-Hua Li, Yi-Fu Liu, En-Wei Hu, Yi-Tsung Lin, Hsu-Feng Lu, Tsuey-Ching Yang, Silvia T. Cardona
Microbiology Spectrum.2023;[Epub] CrossRef
Identification and Validation of Reference Genes for Expression Analysis in Nitrogen-Fixing Bacteria under Environmental Stress
Dylan Parks, Christian Peterson, Woo-Suk Chang
Life.2022; 12(9): 1379. CrossRef
MostSinorhizobium melilotiExtracytoplasmic Function Sigma Factors Control Accessory Functions
Claus Lang, Melanie J. Barnett, Robert F. Fisher, Lucinda S. Smith, Michelle E. Diodati, Sharon R. Long, Craig D. Ellermeier, Claude Bruand, Sarah Ades, Hans-Martin Fischer
mSphere.2018;[Epub] CrossRef

Factors Influencing Preferential Utilization of RNA Polymerase Containing Sigma-38 in Stationary-Phase Gene Expression in Escherichia coli: Eun Young Kim , Min-Sang Shin , Joon Haeng Rhee , Hyon E. Choy; J. Microbiol. 2004;42(2):103-110.; DOI: https://doi.org/2037 [pii]

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Abstract: In order to understand the molecular basis of selective expression of stationary-phase genes by RNA polymerase containing [sigma]^38 (E[sigma]^38) in Escherichia coli, we examined transcription from the stationaryphase promoters, katEP, bolAP, hdeABP, csgBAP, and mcbP, in vivo and in vitro. Although these promoters are preferentially recognized in vivo by E[sigma]^38, they are transcribed in vitro by both E[sigma]^38 and E[sigma]^70 containing the major exponential [sigma], [sigma]^70. In the presence of high concentrations of glutamate salts, however, only E[sigma]^38 was able to efficiently transcribe from these promoters, which supports the concept that the promoter selectivity of [sigma]^38 -containing RNA polymerase is observed only under specific reaction conditions. The examination of 6S RNA, which is encoded by the ssr1 gene in vivo, showed that it reduced E[sigma]^70 activity during the stationary phase, but this reduction of activity did not result in the elevation of E[sigma]^38 activity. Thus, the preferential expression of stationary-phase genes by E[sigma]^38 is unlikely the consequence of selective inhibition of E[sigma]^70 by 6S RNA.

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